WCS MERMAID Fishbelt Dashboard Visualizations

This code provides examples of visualizations shown on the MERMAID dashboard (https://dashboard.datamermaid.org) that use data from the fishbelt protocol.

Getting fishbelt data

Download summary sample event data from MERMAID (https://datamermaid.org), using the mermaidr package (documentation can be found at https://data-mermaid.github.io/mermaidr/).

rm(list = ls()) #remove past stored objects
options(scipen = 999) #turn off scientific notation

####  Load packages and libraries ####
## If this is the first time using mermaidr, install the package through "remotes"
# install.packages("remotes")
# remotes::install_github("data-mermaid/mermaidr")
# install.packages("tidyverse")
# install.packages("plotly") 
# install.packages("htmlwidgets")

library(mermaidr) #package to download data from datamermaid.org
library(tidyverse) #package that makes it easier to work with data
library(plotly) #for interactive plotting
library(htmlwidgets) #for saving plots at html files

#### Get data from MERMAID for creating aggregate visualizations ####
allMermaidSampEventsTBL <- mermaidr::mermaid_get_summary_sampleevents()

Aggregate data - histogram of fish biomass (kg/ha)

This code creates a histogram of the fish biomass data from all the sample events available with permissions of “public summary” or “public”. It includes the total number of surveys (i.e. sample events in MERMAID) and truncates the data at 5000 kg/ha, with any surveys above that grouped into a single bar for “5000+”.

### Fish biomass data - only use relevant data and truncate > 5000 kg/ha
fishbeltSurveySummTBL <- allMermaidSampEventsTBL %>% 
  filter(!is.na(beltfish_biomass_kgha_avg)) %>% 
  mutate(truncBiomass = ifelse(test = beltfish_biomass_kgha_avg > 5000,
                               yes = 5001,
                               no = beltfish_biomass_kgha_avg))

### Create the plot
fishbeltAggHist <-
  plot_ly(data = fishbeltSurveySummTBL,
          x = ~truncBiomass,
          type = 'histogram',
          xbins = list(start = 0, size = 100),
          marker = list(color = "#769fca"),
          height = 450) %>%
  config(displayModeBar = TRUE,
         displaylogo = FALSE,
         modeBarButtonsToRemove = c('zoom','pan', 'select', 'zoomIn', 'zoomOut',
                                    'autoScale', 'resetScale', 'lasso2d',
                                    'hoverClosestCartesian', 'hoverCompareCartesian')) %>% 
  layout(bargap = 0.1,
         xaxis = list(title = "Fish biomass (kg/ha)",
                      linecolor = "black",
                      linewidth = 2,
                      tickmode = "array",
                      ticktext = list("0",
                                      "1000",
                                      "2000",
                                      "3000",
                                      "4000",
                                      "5000+"),
                      tickvals = list(0, 1000, 2000, 3000, 4000, 5000)),
         yaxis = list(title = "Number of surveys",
                      #type = 'log',
                      linecolor = "black",   # Set the y-axis line color to black
                      linewidth = 2),
         annotations = list(
           list(x = 0, y = 1.15, text = "FISH BIOMASS (KG/HA)", showarrow = FALSE, 
                xref = 'paper', yref = 'paper', xanchor = 'left', yanchor = 'top',
                font = list(size = 20)),
           list(x = 0, y = 1.08,
                text = paste0(length(fishbeltSurveySummTBL$beltfish_biomass_kgha_avg),
                             " Surveys"),
                showarrow = FALSE, 
                xref = 'paper', yref = 'paper', xanchor = 'left', yanchor = 'top',
                font = list(size = 12))
         ),
         margin = list(t = 50, b = 75))  # Increase top margin to create more space for title and subtitle

# Visualize the plot
fishbeltAggHist